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                <title>Identification - Formula prediction</title>
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                <h1>Formula prediction</h1>

                <h2>Description</h2>

                <p>
                        This module attempts to calculate all possible molecular formulas for a peak, 
                        using given elemental and heuristic constraints.  For a detailed description of the 
                        functionality and the embedded algorithms, please see the following publication: <br>
                        Pluskal T. et al, Highly Accurate Chemical Formula Prediction Tool Utilizing High-Resolution Mass
                        Spectra, MS/MS Fragmentation, Heuristic Rules, and Isotope Pattern Matching. 
                        <i>Anal Chem</i> (2012), 84(10):4396-403.
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                <p>
                		The module is invoked by selecting a single peak within a peak list:<br>
                        <img src="selection.png">
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                <p>
                		List of formula candidates:<br>
                        <img src="candidates.png">
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                <h4>Method parameters</h4>
                <dl>
                        <dt>Neutral mass</dt>
                        <dd>The neutral mass is calculated from the peak m/z value, its charge and type of ionization adduct.</dd>

                        <dt>m/z tolerance</dt>
                        <dd>Tolerance of the neutral mass for searching the formula.</dd>

                        <dt>Elements</dt>
                        <dd>Elements allowed in the formula and their minimum and maximum counts.</dd>

                        <dt>Element count heuristics</dt>
                        <dd>Selection of heuristic restrictions on element counts.</dd>

                        <dt>RDBE restrictions</dt>
                        <dd>Selection of restrictions on RDBE (rings double bonds) values. .</dd>

                        <dt>Isotope pattern filter</dt>
                        <dd>If selected, only results which fit the required isotope pattern similarity score will be returned.</dd>
                        
						<dt>MS/MS filter</dt>
                        <dd>Restrict the formulas to those that can be interpreted in the peak's MS/MS pattern.</dd>
                        
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